Well, yes. There is little reason for the Red Star to be revealed as a spirit-gathering revivification device if the recently dead were not to appear, I suppose. But what of Tren Krom? Would he just get stuck in a new body too? He's shown that he can use his powers outside of the jelly body, but is he even safe to put in the Red Star if he knows how it works? Does Mata Nui himself know how it works/was supposed to work?
Worth noting that TK is the one that connected death by murderer to the Red Star in the first place.

And I'd presume he's dangerous there too, and that the GB is counting on it so he'll be effective against the Kestora, but perhaps far less so. For one thing, the jelly form was huge, so if he's just downloaded into a humanoid body, he's much smaller, so he'd at least take up less physical space.
If he wanted to throw off the investigators he should not leave carvings at all, since that says "carver" rather than just "random criminal".
Well, I was thinking the fact that he's apparently doing something to the stone foundation of the fortress would inevitably scream "carver" to them anyways, so he would at least want to throw them off as far as his motives. True we don't know for sure how he rigged the foundation to fail, but I think it's likely he severely weakened it with knowledge of stone. Then perhaps a bomb to blow away the final stability remainder.
Velika's thoughts are more "my problem down here will soon be solved" than "I hope my problem up there will be solved by this".
Where does he give any clue as to where the problem is? I figure that since it's already established he's rapidly traveled vast distances, apparently by teleporter (I'm still thinking he stole the Spirit's Wish gate teleporation system, but perhaps it's not tied into the RS), that the location of his goal is not so relevant.
Let's look at some of the quotes. I can think of one that does seem to hurt my theory off the top of my head, maybe, but most of it seems perfectly consistent:
No, what was important about that building was who else was inside it now. Axonn, Brutaka and Toa Helryx, veteran warriors; Makuta Miserix, with all the power that title implied; Artakha, wearer of the Mask of Creation; Toa Tuyet, who was mightier than any of the others knew; and Vezon, gifted with the ability to move through dimensions the way others move through air. So many beings of power, all in one spot … it was quite delicious.
Presuming he's been waiting a long time to stop the Kestora, this makes sense.
So far, he had killed Tren Krom and Karzahni… one a madman, the other a gelatinous mass of hot air. Neither proved to be much of a challenge. The Toa were keeping the whole thing quiet, as they often did. Although the two heroes investigating the murders, Kopaka and Pohatu, had recently vanished, he was not overly concerned. They would turn up eventually. The plan required it.
Interesting he doesn't say anything like "good riddance". Especially if my alternate idea that he hopes the two groups will wipe each other out is true -- maybe he hopes the villains will die, and tries to set some of them first, then as the Kestora are weakened, sends good guys.
Also this last bit was what I thought hurt my theory, but it seems he doesn't know K&P are already on the RS, just "vanished."
In the same way, the sight of Toa Lewa being dragged off by nature-loving Agori was at best a minor obstacle. If need be, he would effect a rescue in some indirect way before the Toa of Air could get into any real jeopardy. The Toa Mata were too important to have their lives sacrificed needlessly. Oh, they would die, eventually, but it would be at a time of his choosing.
This strongly implies it's important they must die in just the right way so they can get teleported. If they didn't, their lives would be sacrificed needlessly. You could still make a case against the theory here though.
No one would ever suspect him, of course. No one ever had. As time passed and things had become clear to him, he had known this time would come.
Under this theory, the "things" would be why good guys weren't coming back, and possibly also that the Kestora were murdering them. And probably more importantly to him, that he would find the Kestora dangerous were he to personally try to go up and pilot the RS now.
Yanno, he might not be thinking "crew" but simply hopes the good guys alone survive for the most part, then after a while get bored with the RS and come back down, leaving it alone or minorly guarded. Then Velika could take it when nobody's looking (except a few guards).
Also, it's quite possible he does NOT want to return to the other GBs but rather wants to flee the planet before Angonce summons them and they may punish him for his choice long ago (or maybe a worse choice that made him flee them into the MU in the first place).
The most powerful would need to be eliminated individually – no point in risking the grand plan because he had missed one, after all – and the rest could be dealt with at leisure. He had expected it to be a time-consuming, if amusing, exercise, a sort of living strategy game in which only he knew the rules.
Now, though, fate seemed to have altered the circumstances. So many of his targets, all in the same place, offered the opportunity to accelerate his timetable – much too good of an opportunity to miss. A little of this, a little of that, and the fortress would be so much rubble … and the universe far better off.
"Eliminated" could be taken against the theory, but I'm running under the assumption that any synonym of murder (of their original bodies) is fair game for him to use in his thoughts. The rest of this fits perfectly. The rules only he knows is what Greg revealed (with the sub-theory that it can pull dead beings in from SM). And "far better off" means ridding it of the truly murderous Kestora and even giving some old good guys a chance to get down to SM, as well as maybe other goals he has that he wants to pursue with hyperdrive.
I thought the Red Star was a booster engine (like the first stage of a multi-stage rocket) and not a hyper drive per se?
I'm thinking of it like a tugboat, which can serve as a booster engine for a larger boat, but only because it is its own engine. And unlike a space shuttle separating rocket, the RS isn't a one-time use, so it's more likely it can function on its own.
Plus, again, it's made by the GBs, and keep in mind the #1 rule about them; Safeguards R Us.
The Kestora say Gaardus is to blame for the system not working. He protests, saying he did not choose to come or go (since he was likely dead the last time). Perhaps it just happened to break when he arrived, or perhaps his teleportation ability interfered with the Red Star's teleportation in some way (or he got it in some sort of freak accident with the machinery, like how Zaktan turned to protodites after the Shadowed One tried to disintegrate him).
I agree with those possibilties; I was thinking along the same lines.

Given that he claims he didn't choose to go, maybe as soon as he was revived, his power automatically interacted with the Send teleporter, breaking it and sending him away to some random place.
They then say the two Toa and Gaardus need to go, as they "got what they came here for". I can only assume this means new bodies, as the Kestora proceed to mention Mata Nui as the destination and were carrying weapons to defend themselves. (In case a revived being got out, like this? I'm just guessing.)
I agree again.

Pohatu interjects, saying that Mata Nui is rubble in the desert. The Kestora worry since they can't send them back anywhere, then say they have too many on board. One mentions dissection to find out why sending them back won't work (maybe because the Matoran Universe itself is not needed as a receiver, as you say, just the intended place for them to live), but they never get further than that.
I take this to mean that they have enforced a sort of space rationing system, since it has limited size compared to the giant robot, and they are allowing some to live, but whenever someone new is revived here, they decide somehow who to kill to keep the ration stable. The send back comment here may simply refer to using their weapons as a threat to force Gaardus to return them the way he brought them, actually -- we might be getting distracted by that and taking it wrongly as referring to the broken Sender. Or maybe the confusing nature of this means that they are confused themselves between Gaardus's teleportation and the broken sender. Their arguing over it in the context of this part fits with that.
From what I gather (and with Pohatu's later line about "Lots of labs. Some old machinery, looks like it’s been jury-rigged a few hundred times."), they are trying to repair the place and just get things working again so that all the darn people will get back where they belong. If they have to permanently kill a few, no problem, they are "just bio-mechs". Amoral, perhaps; uncaring, definitely. I don't see the Kestora as evil just yet, just completely lacking in care for what their experiments might do.
Yeah, that's possible, but then permanently murdering people is generally considered evil.

From their own perspective they might not be evil. But then, my theory is pitting a guy that's willing to kill in order to teleport people, so he need not rationally oppose them fully anyways.
Also, I really think his endgame here is the theorized fully functional hyperdrive, and the Kestora would oppose his takeover of it.
Let's walk through what would happen, assuming the Receiver works on SM.
As he kills more beings like Karzahni, Tren Krom, and the Fortress Folk, the RS is getting more populated.
This forces the Kestora to open fire, eventually, on the new revivals (ha ha pun, get it okay).
This forces the new folks to fight back, and presumably wipe out the Kestora. Kopaka demonstrated at least that the Kestora are not impossible to beat (apparently) by any stretch. Thus most if not all of the people Velika sends survive.
If he then just waits things out, eventually they'll figure out a way to leave the RS, perhaps via Gaardus's teleportation. Maybe Alternate Teridax. Plenty of ways, or maybe someone more inventive will figure out how to fix the teleportation. Maybe even Goldiflocks will be killed and he'll just wave his hand and fix it.

The serial did start out with a mention of him, after all.
Then, once the RS is mostly empty, Velika is free to come in and take it.
I'd like to think of it as on a time-limit as well: If the revive does not occur in time, the being gets wiped in some way. So Jaller and Takanuva would keep their memories, but someone like Lhikan (who is long dead) would start with no memories at all.
Cool idea!
Regarding new Matoran coming into being and Matoran being able to tell you how (as Greg once mentioned)... would this mean that a newly built Matoran recieves a spirit from the Red Star rather than having it created along with the body?
Well, I'm thinking there is a finite amount of this stable energy substance we call spirit in the MU, or at least that it's so difficult to make that that was the original idea and later they had to find a way to make it anyways. (Mata Nui did that is.) So the original idea would be to revive them so you wouldn't always have to make more, but probably there would still be a reserve for the "unfilled needs" reason, which would require new beings with new personalities.
Yanno, somehow all of this also got me thinking about how Krana are organic and the old idea that that might be evidence all the other brains are organic too.
What if what it teleports is just brains, and they're organic, and it's organics that is the difficult material to make? I kinda hinted at this possibility earlier but I was just brainstorming there. As a defined theory, maybe the
only way to make a new brain -- with new personality, genetics-equivalent, etc. -- is for the Turaga to tap into some system that remotely accesses the Mask of Life? It would make the new brain and teleport it. But doing so might come with risks. A glitching "villain" unit might have attention drawn to it because of this activity, and the GBs preferred it to remain very secret.
And I'm presuming that new brains act like stem cells to grow the rest of the organics in a new being, while the mechanical parts are manufactured (possibly materialized with elemental Iron power).
This would explain why a system that circumvents that need might exist.
Instead of tapping into the Mask of Life to bring new life to a new brain, it would teleport up brains from dead bodies (and maybe antidermis), take a bit of the brain material to "seed" the growth of a new brain, transfer the AI/memories/etc. to the new brain, and built a new body for it, then send back.
This would also leave the rest of the original bodies as corpses. Only the brain would be taken, like a Bohrok without a Krana, but because most beings' brains are entirely encased in metal skulls, nobody would ever be likely to notice.
If
this possibility is true, it would rule out final Matoro (but again, that 777 stair thing might counter this up to that point), and again would rule out anybody like Teridax who was physically destroyed. But it would not rule out Skakdi and the like due to any mask rule.
In fact if this was the case I suspect Lhikan would be there just fine -- and that masks just store connections to provide an alternate Send, so the fact that Lhikan's mask was kept would not be a problem at all, but simply would give more time during which he could be revived. I think I like that idea best if only because it rescues Vakama from creepily having 'double-killed' Lhikan by taking the mask, and is more consistent with past understandings of that. Jaller is exactly the same except that his revived body happened to get activated to teleport back down to his mask by Takutanuva.
I also just had yet another theory but in typing the above I forgot it lol. I'm sure it'll come to me...